This is a significant release. There are a large number of changes, which will change your configuration files slightly, but for the better.

The primary changes are

- link input data files can now use one line, instead of two, using the format

chr1 start1 end1 chr2 start2 end2 {options}

- <link> blocks no longer need to be named (e.g. <link mylink> is deprecated)

- colors can be specified with r,g,b values, as well as names

- rules mechanics have changed: importance is optional (rules will be evaluated in order of appearance) and multiple 'flow' parameters are supported (stop, continue, restart, goto). Flow can be triggered on rule pass, fail or always.

- reference to configuration parameters no longer requires __ $CONF{clunky}__ syntax. You can now use conf(param)

- reference to variables in rules no longer requires _START_ syntax. You can now use var(start)

Fixed bug in extend_bin which prevented extend_bin=no from being correctly interpreted.

Fixed bug in testing z-depth for plots.

Fixed bug with angle_offset.

Links with transparency should now show up correctly in SVG.

Plot axes should now show up correctly in SVG.

Fixed a bug which made reversed chromosome segments created with chromosomes_breaks show up in an unintuitive order.

Fixed behaviour of offset when drawing slices. This fixed a bug that made some slice arcs curve the wrong way.

Configuration file syntax __$CONF{a}{b}__ can now be replaced with conf(a,b). eval() is needed if the conf value is used in an expression. For example eval(2*conf(a,b)) instead of __2*$CONF{a}{b}__

Wherever you would use a color name, you can now specify colors using r,g,b or r,g,b,a values. Here 'a' is the alpha channel 0..127 (0=opaque,127=transparent).

color = red color = 250,50,50

Added -randomcolor, just for fun.

Links can be specified on one line in input data file, instead of two

chr1 start1 end1 chr2 start2 end2 {options}

<link> blocks no longer need to be named - they now behave like <plot> blocks.

<links> <link> ... </link> <link> ... </link> ... </links>

Rules are now ordered in two phases. First, all rules with an 'importance' value are placed first, followed by rules that don't have this parameter, in the order that they appear. For example, if the following are rules' importance values ("-" means not defined)

r1 - r2 0 r3 15 r4 - r5 20

the final order will be r5(20),r3(15),r2(0),r1(-),r4(-). Thus, rules don't need the importance parameter at all, if you're happy with their order of appearance.